2-184504896-G-T

Variant names:

• chr2-184504896-G-T
• rs17583433

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0906 in 151,792 control chromosomes in the GnomAD database, including 909 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.091 (909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13736 AN: 151674 Hom.: 905 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0784

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0906 AC: 13751 AN: 151792 Hom.: 909 Cov.: 32 AF XY: 0.0975 AC XY: 7228 AN XY: 74166

African (AFR) AF: 0.0360 AC: 1491 AN: 41472

American (AMR) AF: 0.0583 AC: 885 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1171 AN: 5114

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4814

European-Finnish (FIN) AF: 0.173 AC: 1826 AN: 10562

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0956 AC: 6484 AN: 67852

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0593 Hom.: 85

Bravo AF: 0.0751

Asia WGS AF: 0.225 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.31
PhyloP100		-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17583433; hg19: chr2-185369623;